Genetic and cytogenetic structure of biological diversity and taxonomic interpretation of this structure are currently highly debated among biologists since these problems are important for understanding both biological evolution and functioning the ecosystems, as well as for environmental protection. The authors of the current special issue use the mitochondrial molecular and chromosomal characters (or a combination of these two types of genetic markers) to reveal genetic and cytogenetic structure in several groups of insects belonging to the orders Lepidoptera, Neuroptera and Hemiptera. Then they use the data obtained for testing taxonomic hypotheses and providing insight into systematics and phylogenetics of the studied groups.